Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate AO353_19305 AO353_19305 3-methylcrotonyl-CoA carboxylase
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19305 Length = 653 Score = 582 bits (1499), Expect = e-170 Identities = 326/659 (49%), Positives = 432/659 (65%), Gaps = 22/659 (3%) Query: 7 SIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSY 66 +++++L+ANRGEIACR+ R+A+ALG +VAV SD D A HV AD AV++G A A SY Sbjct: 3 TLRKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVRMADEAVNIGPAAVAQSY 62 Query: 67 LRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAK 126 L II AAL SGA AIHPGYGFLSENA+FA AC +AG+ F+GP AAI+ MGSK +K Sbjct: 63 LNSAAIIDAALRSGADAIHPGYGFLSENAEFATACAQAGITFIGPDPAAIELMGSKRLSK 122 Query: 127 ALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186 M AGVP + GY G QD T REA RIGYP+++KA+AGGGG+GM++V EL Sbjct: 123 IAMLAAGVPCIGGYQGAEQDDATLSREAERIGYPLMIKASAGGGGRGMRLVHTADELLAQ 182 Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246 + +A+ EA AFG +++E+ L++PRHVEIQ+F D+HG+ +YL ERDCSIQRRHQKV+E Sbjct: 183 IRTARSEALHAFGSDELILEQALIEPRHVEIQLFGDQHGNLIYLGERDCSIQRRHQKVIE 242 Query: 247 EAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVT 306 EAP P + AELR AMGEAA++A +A+ YVGAGTVEFLLD RGQF+F+EMNTRLQVEHPVT Sbjct: 243 EAPCPVMTAELRDAMGEAALKAGRAVNYVGAGTVEFLLDARGQFYFLEMNTRLQVEHPVT 302 Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366 E ITGLDLVAWQ+ VA G LPL QEQV L GHA+EVRLYAEDP DFLP +GR+M + E Sbjct: 303 EMITGLDLVAWQLDVAAGLPLPLRQEQVELKGHAMEVRLYAEDPAQDFLPQTGRIMRW-E 361 Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426 A G R+D G+ EG +VSPFYDP+L K+IA+G TREEAR++LL + ++++ GL+TN Sbjct: 362 PALADGVRIDHGLLEGQQVSPFYDPLLGKIIAYGATREEARRKLLRAVQDSALLGLQTNQ 421 Query: 427 AFLRRILGHPAFAAAELDTGFIARHQDD--LLPAPQALPEHFWQAAAEAWLQSEPGHRRD 484 L +L HP F A + +TGFIA+H D L + E A A + QS H Sbjct: 422 RLLAGLLEHPQFIAGDFNTGFIAQHFADHPSLHSHAPTAEELAIATALFYQQSAGAHPPG 481 Query: 485 -----DDPHSPWSR-----NDGWRSALAR--ESDLMLRCRDERRCVRLRHASPSQYRLDG 532 ++ ++P + D W + + + L+++ E ++L + L+ Sbjct: 482 LAGWRNNANAPLLQQIGLNGDRWSTEVTALPDGQLVIQVAGETLQLKLLDINARSANLE- 540 Query: 533 DDLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAPMNGS 592 ++G+ RR A QL+L L ++ + G L APM+G+ Sbjct: 541 ------INGIRRRYAYQLAAGQLWLFTRPGSLLLQDQTLAPVSSQVGTSTGTLKAPMDGA 594 Query: 593 IVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLVELD 651 IV VLV G +V G L+VLEAMKMEH ++A GV+K L S G+ V+ L+E++ Sbjct: 595 IVDVLVSEGSSVTKGQLLLVLEAMKMEHPLKAGIDGVIKRLQVSPGDQVKNRQILLEVE 653 Lambda K H 0.319 0.135 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 997 Number of extensions: 35 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 655 Length of database: 653 Length adjustment: 38 Effective length of query: 617 Effective length of database: 615 Effective search space: 379455 Effective search space used: 379455 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory